Rasmus Nielsen

About

Rasmus Nielsen is a Professor of Integrative Biology, Statistics, and a member of the Center for Computational Biology at UC Berkeley. His research focuses on the statistical and computational aspects of evolutionary theory and genetics. A central problem in his work is understanding the molecular basis of evolutionary adaptation, specifically what occurs at the molecular level as one species transforms into another over evolutionary time. To investigate these questions, he has developed various computational methods and applied them to large-scale genomic data, including genomic comparisons of humans and chimpanzees. Nielsen has also contributed to the development of statistical methods in population genetics, medical genetics, phylogenetics, molecular ecology, and molecular evolution. His work aims to deepen the understanding of evolutionary processes through computational and statistical approaches, leveraging large genomic datasets to elucidate the mechanisms underlying adaptation and evolution.

Research topics

• Ecology
• Geography
• Demography
• Biology
• Archaeology

Selected publications

• Massive haplotypes underlie ecotypic differentiation in sunflowers

  Nature · 2020-07-08 · 515 citations

  articleOpen access

  Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2–4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1–100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecolo…

  PublisherOA PDFDOI

• Population genomics of the Viking world

  Nature · 2020-09-16 · 353 citations

  articleOpen accessCorresponding
  PublisherOA PDFDOI

• Population genomics of post-glacial western Eurasia

  Nature · 2024 · 199 citations

  . Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone…

  PublisherOA PDFDOI

• Population genomics of postglacial western eurasia

  bioRxiv (Cold Spring Harbor Laboratory) · 2022 · 97 citations

  Summary Western Eurasia witnessed several large-scale human migrations during the Holocene 1–5 . To investigate the cross-continental impacts we shotgun-sequenced 317 primarily Mesolithic and Neolithic genomes from across Northern and Western Eurasia. These were imputed alongside published data to obtain diploid genotypes from >1,600 ancient humans. Our analyses revealed a ‘Great Divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers (HGs) were highly…

  PublisherOA PDFDOI

• ASTER: A Package for Large-Scale Phylogenomic Reconstructions

  Molecular Biology and Evolution · 2025-07-16 · 35 citations

  articleOpen access

  Many algorithms are available for inferring species trees from various input types while accounting for gene tree discordance. Several quartet-based species tree inference methods, collectively known as the ASTRAL family, are based on similar ideas and are in wide use. Here, we integrate all ASTRAL-like methods into a single package called ASTER, comprising several tools, each designed for a different input type: (i) ASTRAL for single-copy gene tree topologies, (ii) weighted ASTRAL (wASTRAL) for…

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01GM116044

  NIH · $2.4M · 2021

• Berkeley Training Program in Genomics and Computational Biology

  NIH · $12.6M · 2000–2030

• NIH Grant R01HG003229

  NIH · $4.0M · 2014

Frequent coauthors

• Eske Willerslev

  University of Cambridge

  317 shared

• Thorfinn Sand Korneliussen

  University of Copenhagen

  178 shared

• Morten E. Allentoft

  146 shared

• J. Víctor Moreno-Mayar

  University of Lausanne

  141 shared

• Martin Sikora

  University of Copenhagen

  135 shared

• Ludovic Orlando

  Université Toulouse III - Paul Sabatier

  118 shared

• Jun Wang

  Chinese Academy of Sciences

  102 shared

• Andrés Ingason

  Lundbeck Foundation

  93 shared

Labs

• Center for Computational BiologyPI

Similar researchers at University of California, Berkeley

• Daniel Rokhsarh-155
• Adam Arkinh-135
• Marc Hellersteinh-105